If you're using FTP to access files on your server, it's easy for someone to hack and maliciously use that connection. Be sure to use secure FTP software for file transfers.
In essence, when you do normal FTP connections, you send your username and password to your server in an insecure manner. Anybody could sense what those values were with very simple hacking tools. Once they have your username and password, they can log on any time they wish and upload and download files.
The solution is to get a secure FTP software package. This runs on both the server and client end, and makes sure that all transmissions between the two ends are secure.
One that I have tested is eFTP -
eFTP Download Site
It's free for personal use, and very easy to use.
However you set up your file transmissions, make sure that it is done with security in mind!